RetrogeneDB ID: retro_mmul_2207

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:15143554..15144259(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000006838
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1A1
• Ensembl ID: ENSMMUG00000001758
• Aliases: None
• Description: casein kinase I isoform alpha [Source:RefSeq peptide;Acc:NP_001248164]

Sequence

>retro_mmul_2207
AATTTCTGTTCAAGAAGGTTCACAATGAAAACTGTACTTATATTAGCTGACCAGATGATCAGTAGAATTGAACATGTGCA
TAAAAAGAATTTTATACACGGAGCCATTAAACCAGATAACTTCCTAATGGATATTGGGCGTCACTGTAGTAAGTTATTCC
TTATTGATTTTGGTTTGGCCAAAAAGTACAGAGACAACAGGACAAGGCAACACAGGCCATACAGAGAAGATAAAAACCTC
ACTGGCATTGCCCTATATGCTACCATCAGTGCACATCTTGGTATTGAGCAGAGTCACCAGGATGACAAGGAATCATTAGG
ATATGTTTTGATGTATTTTAATAGAACCAGCCTGCCATGGCGAGGGCTAAAGGCTGCAACAAAGAAACAAAAATATGAAA
AGATTAGTGAAAAGATGTCCACTCCTGCTGAAGTTTTACGTAAGGGGTTTCCTGCAGAATTTGCCATATACTTAAACTAT
TGTCGTGGGCTACACTTTGAGAAAGCCCCAGATTGCATGTGTCTGAGGCAGCTACTCTTCATTCTTTTCAGGACCCTGAG
CCATCAATATGACTACACATTTGACTGGACAATGTTAAAGCAGAAAGCAGCCCAGCAGGCAGCCTCTTCTACTGGGCAGG
GGCAGCAGGCCCCAACCCCAACAGGTAAGCAACCTGACAAAACCAAGAGTAACATGAAAGGTTTC

Alignment

ORF - retro_mmul_2207 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.29 %
• Parental protein coverage: 70.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQ
          NFCSRRFTMKTVL.LADQMISRIE.VH.KNFIH..IKPDNFLM.IGRHC.KLFLIDFGLAKKYRDNRTRQ
Retrocopy NFCSRRFTMKTVLILADQMISRIEHVHKKNFIHGAIKPDNFLMDIGRHCSKLFLIDFGLAKKYRDNRTRQ

Parental  HIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKM
          H.PYREDKNLTG.A.YA.I.AHLGIEQS..DD.ESLGYVLMYFNRTSLPW.GLKAATKKQKYEKISE.KM
Retrocopy HRPYREDKNLTGIALYATISAHLGIEQSHQDDKESLGYVLMYFNRTSLPWRGLKAATKKQKYEKISE-KM

Parental  STPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQKAAQQAAS
          STP.EVL.KGFPAEFA.YLNYCRGL.FE.APD.M.LRQL..ILFRTL.HQYDYTFDWTMLKQKAAQQAAS
Retrocopy STPAEVLRKGFPAEFAIYLNYCRGLHFEKAPDCMCLRQLLFILFRTLSHQYDYTFDWTMLKQKAAQQAAS

Parental  SSGQGQQAQTPTGKQTDKTKSNMKGF
          S.GQGQQA.TPTGKQ.DKTKSNMKGF
Retrocopy STGQGQQAPTPTGKQPDKTKSNMKGF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.11 RPM	71.26 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	67.43 RPM
SRP007412_cerebellum	0.00 RPM	90.15 RPM
SRP007412_heart	0.00 RPM	59.12 RPM
SRP007412_kidney	0.00 RPM	68.19 RPM
SRP007412_liver	0.20 RPM	29.89 RPM
SRP007412_testis	5.80 RPM	69.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2207 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2207 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1178

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207 , retro_mmul_295,
Macaca mulatta	ENSMMUG00000006620	1 retrocopy	retro_mmul_1195,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,